rs34138162

chr10-129466959-C-Achr10-129466959-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0395 in 152,100 control chromosomes in the GnomAD database, including 195 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.039 (195 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.425

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BS1: Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.0395 (6002/152100) while in subpopulation AMR AF= 0.0515 (787/15296). AF 95% confidence interval is 0.0485. There are 195 homozygotes in gnomad4. There are 3176 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 195 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0395 AC: 6005 AN: 151990 Hom.: 195 Cov.: 33

Gnomad AFR AF: 0.00770

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.0516

Gnomad ASJ AF: 0.0953

Gnomad EAS AF: 0.0136

Gnomad SAS AF: 0.0273

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0447

Gnomad OTH AF: 0.0398

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0395 AC: 6002 AN: 152100 Hom.: 195 Cov.: 33 AF XY: 0.0427 AC XY: 3176 AN XY: 74376

Gnomad4 AFR AF: 0.00768

Gnomad4 AMR AF: 0.0515

Gnomad4 ASJ AF: 0.0953

Gnomad4 EAS AF: 0.0132

Gnomad4 SAS AF: 0.0274

Gnomad4 FIN AF: 0.116

Gnomad4 NFE AF: 0.0447

Gnomad4 OTH AF: 0.0403

Alfa AF: 0.0490 Hom.: 40

Bravo AF: 0.0347

Asia WGS AF: 0.0290 AC: 99 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
Cadd	Benign	1.6
Dann	Benign	0.57

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs34138162; hg19: chr10-131265223;